CDD: a database of conserved domain alignments with links to domain three-dimensional structure

@article{MarchlerBauer2002CDDAD,
  title={CDD: a database of conserved domain alignments with links to domain three-dimensional structure},
  author={Aron Marchler-Bauer and Anna R. Panchenko and Benjamin A. Shoemaker and Paul A. Thiessen and Lewis Y. Geer and Stephen H. Bryant},
  journal={Nucleic acids research},
  year={2002},
  volume={30 1},
  pages={
          281-3
        }
}
The Conserved Domain Database (CDD) is a compilation of multiple sequence alignments representing protein domains conserved in molecular evolution. It has been populated with alignment data from the public collections Pfam and SMART, as well as with contributions from colleagues at NCBI. The current version of CDD (v.1.54) contains 3693 such models. CDD alignments are linked to protein sequence and structure data in Entrez. The molecular structure viewer Cn3D serves as a tool to interactively… 
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CDD: specific functional annotation with the Conserved Domain Database
TLDR
NCBI's Conserved Domain Database is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution, and provides annotation of domain footprints and conserved functional sites on protein sequences.
CDD: a curated Entrez database of conserved domain alignments
TLDR
The Conserved Domain Database (CDD), which mirrors the publicly available domain alignment collections SMART and PFAM, and now also contains alignment models curated at NCBI, is now indexed as a separate database within the Entrez system and linked to other Entrez databases such as MEDLINE(R).
CDD: a Conserved Domain Database for protein classification
TLDR
The progress of the curation effort and associated improvements in the functionality of the CDD information retrieval system are reported on.
CDD: a Conserved Domain Database for the functional annotation of proteins
NCBI’s Conserved Domain Database (CDD) is a resource for the annotation of protein sequences with the location of conserved domain footprints, and functional sites inferred from these footprints. CDD…
CDD/SPARCLE: the conserved domain database in 2020
As NLM's Conserved Domain Database (CDD) enters its 20th year of operations as a publicly available resource, CDD curation staff continues to develop hierarchical classifications of widely…
NCBI's Conserved Domain Database and Tools for Protein Domain Analysis
TLDR
The CDD maintains both live search capabilities and an archive of pre‐computed domain annotations for a selected subset of sequences tracked by the NCBI's Entrez protein database, which can be retrieved or computed for a single sequence using CD‐Search or in bulk using Batch CD‐ search, or computed via standalone RPS‐BLAST plus the rpsbproc software package.
CDART: protein homology by domain architecture.
The Conserved Domain Architecture Retrieval Tool (CDART) performs similarity searches of the NCBI Entrez Protein Database based on domain architecture, defined as the sequential order of conserved…
3. Macromolecular Structure Databases
TLDR
To enable scientists to accomplish these tasks, NCBI has integrated MMDB and CDD into the Entrez retrieval system and sequences derived from MMDB structures have been included in the BLAST databases.
Annotation of functional sites with the Conserved Domain Database
TLDR
It is observed that CDD-based site annotation complements existing site annotation in many cases, which may, in part, originate from CDD's curation practice of collecting sites conserved across diverse taxa and supported by evidence from multiple 3D structures.
Improving protein structure similarity searches using domain boundaries based on conserved sequence information
TLDR
Alternative domains, which have significantly different secondary structure composition from those based on structurally compact units, were identified based on the alignment footprints of curated protein sequence domain families and are in the process of inclusion into the VAST search and MMDB resources in the NCBI Entrez system.
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